Probably because Leonor's confession to involvement came before she was incarcerated.
First story was that Leonor hit the child's head off a wall causing death. Joćo then admitted to disposing of the body out back initially. Joćo backed up this story but couldn't find any remains.
Second story Joćo told was that he buried the little girl near the river. Later still it morphed into feeding her to the pigs.
Third story by Leonor was a belated attempt to influence her sentence by claiming she would at last reveal the truth. She claimed that Joana died when an attempted child trafficking deal concocted by Joćo went wrong. She claimed Joćo told her that he put remains in car before sending it off to a crusher. In each case, no remains of the little girl were ever found.
IMO the 'claims' of what happened to the child were put to her and her brother by the PJ. Once a confession had been obtained, why would LC refuse to say where the body was? That makes no sense. The obvious reason is because she didn't know - and all the torturing in the world could not make any difference to that.
Unfortunately for Amaral and the PJ - the Prison authorities would not play ball, and refused to help them to cover up the torture by agreeing to say her injuries happened at the prison.
IMO the trial was a farce and as public opinion had been whipped up to lynch mob level via the press by the time it came to court - it would have been a brave jury member who found her 'not guilty.'
How anyone can support ANY conviction where a court has deemed torture took place during interrogation and that attempts were made by the Police to cover it up is beyond my comprehension.